Removed GATK use of distributed parallelism framework.

Moved distributed GATK prototype code into distributedutils, separating from threading package

public/java/src/org/broadinstitute/sting/gatk/executive/LinearMicroScheduler.java

@@ -49,7 +49,7 @@ public class LinearMicroScheduler extends MicroScheduler {
         Accumulator accumulator = Accumulator.create(engine,walker);
 
         int counter = 0;
-        for (Shard shard : processingTracker.onlyOwned(shardStrategy, engine.getName())) {
+        for (Shard shard : shardStrategy ) {
             if ( shard == null ) // we ran out of shards that aren't owned
                 break;
 

public/java/src/org/broadinstitute/sting/gatk/executive/MicroScheduler.java

@@ -39,14 +39,10 @@ import org.broadinstitute.sting.gatk.traversals.*;
 import org.broadinstitute.sting.gatk.walkers.*;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
-import org.broadinstitute.sting.utils.threading.*;
 
 import javax.management.JMException;
 import javax.management.MBeanServer;
 import javax.management.ObjectName;
-import java.io.FileNotFoundException;
-import java.io.FileOutputStream;
-import java.io.PrintStream;
 import java.lang.management.ManagementFactory;
 import java.util.Collection;
 
@@ -83,8 +79,6 @@ public abstract class MicroScheduler implements MicroSchedulerMBean {
     private final MBeanServer mBeanServer;
     private final ObjectName mBeanName;
 
-    protected GenomeLocProcessingTracker processingTracker;
-
     /**
      * MicroScheduler factory function.  Create a microscheduler appropriate for reducing the
      * selected walker.
@@ -98,11 +92,6 @@ public abstract class MicroScheduler implements MicroSchedulerMBean {
      * @return The best-fit microscheduler.
      */
     public static MicroScheduler create(GenomeAnalysisEngine engine, Walker walker, SAMDataSource reads, IndexedFastaSequenceFile reference, Collection<ReferenceOrderedDataSource> rods, int nThreadsToUse) {
-        if (engine.getArguments().processingTrackerFile != null) {
-            if ( walker instanceof ReadWalker )
-                throw new UserException.BadArgumentValue("C", String.format("Distributed GATK processing not enabled for read walkers"));
-        }
-
         if (walker instanceof TreeReducible && nThreadsToUse > 1) {
             if(walker.isReduceByInterval())
                 throw new UserException.BadArgumentValue("nt", String.format("The analysis %s aggregates results by interval.  Due to a current limitation of the GATK, analyses of this type do not currently support parallel execution.  Please run your analysis without the -nt option.", engine.getWalkerName(walker.getClass())));
@@ -157,33 +146,6 @@ public abstract class MicroScheduler implements MicroSchedulerMBean {
         catch (JMException ex) {
             throw new ReviewedStingException("Unable to register microscheduler with JMX", ex);
         }
-
-        //
-        // create the processing tracker
-        //
-        if ( engine.getArguments().processingTrackerFile != null ) {
-            logger.warn("Distributed GATK is an experimental engine feature, and is likely to not work correctly or reliably.");
-            if ( engine.getArguments().restartProcessingTracker && engine.getArguments().processingTrackerFile.exists() ) {
-                engine.getArguments().processingTrackerFile.delete();
-                logger.info("Deleting ProcessingTracker file " + engine.getArguments().processingTrackerFile);
-            }
-
-            PrintStream statusStream = null;
-            if ( engine.getArguments().processingTrackerStatusFile != null ) {
-                try {
-                    statusStream = new PrintStream(new FileOutputStream(engine.getArguments().processingTrackerStatusFile));
-                } catch ( FileNotFoundException e) {
-                    throw new UserException.CouldNotCreateOutputFile(engine.getArguments().processingTrackerStatusFile, e);
-                }
-            }
-
-            ClosableReentrantLock lock = new SharedFileThreadSafeLock(engine.getArguments().processingTrackerFile, engine.getArguments().processTrackerID);
-            processingTracker = new FileBackedGenomeLocProcessingTracker(engine.getArguments().processingTrackerFile, engine.getGenomeLocParser(), lock, statusStream) ;
-            logger.info("Creating ProcessingTracker using shared file " + engine.getArguments().processingTrackerFile + " process.id = " + engine.getName() + " CID = " + engine.getArguments().processTrackerID);
-        } else {
-            // create a NoOp version that doesn't do anything but say "yes"
-            processingTracker = new NoOpGenomeLocProcessingTracker();
-        }
     }
 
     /**

public/java/src/org/broadinstitute/sting/utils/distributedutils/ClosableReentrantLock.java

@@ -1,4 +1,4 @@
-package org.broadinstitute.sting.utils.threading;
+package org.broadinstitute.sting.utils.distributedutils;
 
 import java.util.concurrent.locks.ReentrantLock;
 

public/java/src/org/broadinstitute/sting/utils/distributedutils/FileBackedGenomeLocProcessingTracker.java

@@ -1,4 +1,4 @@
-package org.broadinstitute.sting.utils.threading;
+package org.broadinstitute.sting.utils.distributedutils;
 
 import org.apache.log4j.Logger;
 import org.broadinstitute.sting.utils.GenomeLocParser;

public/java/src/org/broadinstitute/sting/utils/distributedutils/GenomeLocProcessingTracker.java

@@ -1,4 +1,4 @@
-package org.broadinstitute.sting.utils.threading;
+package org.broadinstitute.sting.utils.distributedutils;
 
 import net.sf.picard.reference.IndexedFastaSequenceFile;
 import org.apache.log4j.Logger;

public/java/src/org/broadinstitute/sting/utils/distributedutils/NoOpGenomeLocProcessingTracker.java

@@ -1,4 +1,4 @@
-package org.broadinstitute.sting.utils.threading;
+package org.broadinstitute.sting.utils.distributedutils;
 
 import java.util.Collection;
 import java.util.Collections;

public/java/src/org/broadinstitute/sting/utils/distributedutils/ProcessingLoc.java

@@ -1,4 +1,4 @@
-package org.broadinstitute.sting.utils.threading;
+package org.broadinstitute.sting.utils.distributedutils;
 
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.HasGenomeLocation;

public/java/src/org/broadinstitute/sting/utils/distributedutils/SharedFileLock.java

@@ -1,4 +1,4 @@
-package org.broadinstitute.sting.utils.threading;
+package org.broadinstitute.sting.utils.distributedutils;
 
 import org.apache.log4j.Logger;
 import org.apache.lucene.store.*;

public/java/src/org/broadinstitute/sting/utils/distributedutils/SharedFileThreadSafeLock.java

@@ -1,4 +1,4 @@
-package org.broadinstitute.sting.utils.threading;
+package org.broadinstitute.sting.utils.distributedutils;
 
 import org.apache.log4j.Logger;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;

public/java/src/org/broadinstitute/sting/utils/distributedutils/SharedMemoryGenomeLocProcessingTracker.java

@@ -1,4 +1,4 @@
-package org.broadinstitute.sting.utils.threading;
+package org.broadinstitute.sting.utils.distributedutils;
 
 import java.io.PrintStream;
 import java.util.ArrayList;

public/java/src/org/broadinstitute/sting/utils/distributedutils/package-info.java

@@ -0,0 +1,28 @@
+/*
+ * Copyright (c) 2011, The Broad Institute
+ *
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the "Software"), to deal in the Software without
+ * restriction, including without limitation the rights to use,
+ * copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the
+ * Software is furnished to do so, subject to the following
+ * conditions:
+ *
+ * The above copyright notice and this permission notice shall be
+ * included in all copies or substantial portions of the Software.
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+ * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+ * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+ * OTHER DEALINGS IN THE SOFTWARE.
+ */
+
+/**
+ * Utilities for prototype distributed GATK.  No longer in use in the codebase
+ */
+package org.broadinstitute.sting.utils.distributedutils;

public/java/test/org/broadinstitute/sting/utils/distributedutils/GenomeLocProcessingTrackerUnitTest.java

@@ -1,5 +1,5 @@
 // our package
-package org.broadinstitute.sting.utils.threading;
+package org.broadinstitute.sting.utils.distributedutils;
 
 
 // the imports for unit testing.
@@ -7,9 +7,9 @@ package org.broadinstitute.sting.utils.threading;
 
 import net.sf.picard.reference.IndexedFastaSequenceFile;
 import org.broadinstitute.sting.BaseTest;
-import org.broadinstitute.sting.gatk.iterators.GenomeLocusIterator;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocParser;
+import org.broadinstitute.sting.utils.distributedutils.*;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.testng.Assert;
 import org.testng.annotations.*;